Comparative transcriptomics discovers the genetic basis of contrasting waterlogging tolerance between two cultivated jute species

Abstract

Farmers prefer dark jute (Corchorus olitorius var. O-9897) to white jute (Corchorus capsularis var. CVL-1) because dark jute produces more bast fiber and has greater fiber strength. Crossing incompatibility between these two jute species is the main genetic barrier to transfer waterlogging-tolerant capability from white jute to dark jute. So, to develop a waterlogging-tolerant dark jute variety, gene(s) of interest for certain morphological, anatomical, and physiological features must be transferred from white jute to dark jute without the use of traditional crossing techniques. Therefore, we investigated the comparative gene expressions of CVL-1 and O-9897 tap roots using RNA-Seq and qRT-PCR techniques as well as observed the morphological, histological and physiological behavior under waterlogging treatments. CVL-1 develops schizogenous aerenchyma for oxygen storage, as well as vascular tissues in its adventitious roots for moving water and nutrients from the water solution to the stem, which keeps its tap root less active and so saves more energy in its tap roots. O-9897, on the other hand, degrades its adventitious roots with lysigenous aerenchyma, which results in the formation of no vascular tissues. Thus, O-9897 solely uses its adventitious roots for oxygen storage, while its tap roots are used for water and nutrient transfer, resulting in constant energy depletion in O-9897 tap roots. Consequently, CVL-1 can maintain its normal growth and O-9897 diminishes its bast fiber yield with the lack of energy. The key genes involved in the biogenesis of energy and phytohormones have been more inducing in CVL-1 than O-9897. ATP-producing glycolytic enzyme, phosphoglycerate kinase (CCACVL1_10615) showed remarkable upregulation in CVL-1 while missing in O-9897, playing a vital role in CVL-1 waterlogging tolerance. Our findings reveal a novel mechanism of waterlogging tolerance in white jute, which can be applied to the development of waterlogging-tolerant dark jute varieties in the future.